diff ms2pf_it.xml @ 0:b58b229c4cbf draft

planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ms2pf_it.xml	Fri Mar 03 14:10:24 2023 +0000
@@ -0,0 +1,144 @@
+<tool id="ms_to_peakforest_it" name="MS To PeakForest IT" tool_type="interactive" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+    <description>
+        adds you MS spectrum to peakforest.
+    </description>
+    <macros>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="3.10">python</requirement>
+        <requirement type="package">pyyaml</requirement>
+    </requirements>
+    <entry_points>
+        <entry_point name="MS to PeakForest, with ${','.join(str(i.name) for i in $input)}" requires_domain="True">
+            <port>8000</port>
+            <url>/</url>
+        </entry_point>
+    </entry_points>
+    <version_command>
+<![CDATA[
+python3 '$__tool_directory__/server.py' --version | head -n 1
+]]>
+    </version_command>
+    <command>
+@MS2PF_COMMON_CMD@
+    </command>
+    <inputs>
+        <expand macro="ms2pf_inputs" />
+    </inputs>
+    <outputs>
+        <data name="ms2pfout" format="txt"
+            label="${tool.name} on ${','.join(i.name for i in $input)}"
+        />
+        <data name="json_output" format="json"
+            label="JSON ${tool.name} on ${','.join(i.name for i in $input)}.json"
+        >
+            <filter>do_output_json</filter>
+        </data>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+<![CDATA[
+.. class:: infomark
+
+**Authors** Lain Pavot ([e-mail])
+
+.. class:: infomark
+
+---------------------------------------------------
+
+==============
+MS2 validation
+==============
+
+-----------
+Description
+-----------
+
+
+-----------------
+Workflow position
+-----------------
+
+--------------
+Upstream tools
+--------------
+
++-------------------------+-----------------+--------+------------+
+| Name                    |  output file    | format |  parameter |
++=========================+=================+========+============+
+| ms2snoop                |       tsv       |   TSV  |    NA      |
++-------------------------+-----------------+--------+------------+
+| abinitfragnot           |       tsv       |   TSV  |    NA      |
++-------------------------+-----------------+--------+------------+
+
+----------------
+Downstream tools
+----------------
+
++-------------------------+-----------------+--------+------------+
+| Name                    |  output file    | format |  parameter |
++=========================+=================+========+============+
+| NA                      |       NA        |   NA   |    NA      |
++-------------------------+-----------------+--------+------------+
+
+
+-----------
+Input files
+-----------
+
++----------------------------------------------+------------+
+| Parameter : num + label                      |   Format   |
++===========================+==================+============+
+| Output from ms2snoop or fragnot              |   TSV,CSV  |
++----------------------------------------------+------------+
+
+----------
+Parameters
+----------
+
+input
+  | The file to process. Should contain spectra with mz, intensities and
+  annotations
+
+method
+  | The method parameter tells which method was used. The value will
+    be the default value in the peakforest form.
+
+peakforest-url
+  | The peakforest-url parameter tells which instance of peakforest to
+    interact with
+
+scan_type
+  | The scan_type parameter which kind of scan was used. The value will
+    be the default value in the peakforest form.
+
+polarity
+  | The polarity parameter which polarity was used. The value will
+    be the default value in the peakforest form.
+
+name
+  | The name parameter provides names each spectra.
+
+
+------------
+Output files
+------------
+
+There is not output file. When you run this tool, keep waiting until the
+« click here to display » link appears.
+
+Click on the link to display peakforest form.
+
+--------------
+Changelog/News
+--------------
+
+1.0.0
+  | First version, published on the toolshed.
+
+]]>
+    </help>
+</tool>